From 01a9b1c63b4a2c4e37a6f904fe27d24b57f4332d Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 16 Sep 2009 08:33:56 +0000
Subject: [PATCH] Fix for problem where err stream remapped to output stream in
 certain cases, (hopefully) completing Matt's hat trick of fail.  Thanks, unit
 tests.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1634 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/io/OutputTracker.java    | 2 +-
 .../broadinstitute/sting/gatk/io/OutputTrackerTest.java    | 7 ++-----
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
index 87fe2c2a9..cbf1f8004 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
@@ -75,7 +75,7 @@ public abstract class OutputTracker {
 
             errStub = (errFileName != null) ? new OutputStreamStub(new File(errFileName))
                                             : new OutputStreamStub(System.err);
-            addOutput(errStub,new OutputStreamStorage(outStub));
+            addOutput(errStub,new OutputStreamStorage(errStub));
         }
     }
 
diff --git a/java/test/org/broadinstitute/sting/gatk/io/OutputTrackerTest.java b/java/test/org/broadinstitute/sting/gatk/io/OutputTrackerTest.java
index f132df6b7..0a34329df 100755
--- a/java/test/org/broadinstitute/sting/gatk/io/OutputTrackerTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/io/OutputTrackerTest.java
@@ -3,10 +3,7 @@ package org.broadinstitute.sting.gatk.io;
 import org.junit.Test;
 import org.junit.After;
 import org.junit.Assert;
-import org.broadinstitute.sting.utils.io.RedirectingOutputStream;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.io.OutputTracker;
-import org.broadinstitute.sting.gatk.io.DirectOutputTracker;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 
 import java.io.File;
@@ -81,7 +78,7 @@ public class OutputTrackerTest extends BaseTest {
         Assert.assertSame("OutputTracker: Error stream incorrectly initialized.", System.err, errStream.getOutputStream());
     }
 
-    //@Test
+    @Test
     public void testErrorStreamAlone() throws FileNotFoundException {
         OutputTracker ot = new DirectOutputTracker();
         ot.initializeCoreIO(null,ERROR_FILENAME);
@@ -102,7 +99,7 @@ public class OutputTrackerTest extends BaseTest {
         Assert.assertEquals("OutputTracker: Written error text is incorrect", errText, ERROR_TEXT);
     }
 
-    //@Test
+    @Test
     public void testIndependentStreams() throws FileNotFoundException {
         OutputTracker ot = new DirectOutputTracker();
         ot.initializeCoreIO(OUTPUT_FILENAME,ERROR_FILENAME);